MP autophagy

[gocentral]

Today I am annotating autophagy genes. Before I begin I have a question. I wondered why autphagy is not a child of "protein targeting to vacuole"

if autophagy is the non-constituitve pathway of vacuolar tagettign

(CVT pathway has the protei targeting to vacuple parent)

and the final steps are shared......

Reported by: ValWood

Original Ticket: geneontology/ontology-requests/6721

[gocentral]

I will probably have more questions from my quick scan of the paper and the avaiable terms I am uploading this useful figure which I got from the SGD website:

Original comment by: ValWood

[gocentral]

sorry the file was too large but http:/www.landesbioscience.com/journals/autophagy/index.php

Original comment by: ValWood

[gocentral]

Autophagy is not a child of "protein targeting to vacuole" because autophagy encompasses a lot more than just moving proteins to the vacuole; other macromolecules are also eaten, and the actual degradation is not a type or part of protein targeting.

m

Original comment by: mah11

[gocentral]

OK I guess I can get around this by making a concurrent annotation to protein targeting to vacuole for the autophagy pathway.

Original comment by: ValWood

[gocentral]

If you want, we can also add a term for "protein targeting to vacuole involved in autophagy"; could also be a parent of CVT pathway.

Original comment by: mah11

[gocentral]

I was going to aks that next, its the only thing on my list so far, so yes please V

Original comment by: ValWood

[gocentral]

added protein targeting to vacuole involved in autophagy GO:0071211

I'll leave this open for anything else related ...

Original comment by: mah11

[gocentral]

• labels: --> Other term-related request
• milestone: --> 224410
• assigned_to: nobody --> gomidori

Original comment by: mah11

[gocentral]

Hi,

Can you please hold off on committing this term. We will think about this and comment by next week.

Thanks,

Rama

Original comment by: rbalakri

[gocentral]

Hi Midori,

What would all the parents for "protein targeting to vacuole involved in autophagy" GO:0071211 be? In addition to thinking about the term itself, we just want to make sure that there would be no TPVs between autophagy and CVT.

Thanks, -Julie

Original comment by: juliep

[gocentral]

Hi,

The parents of the new term would be is_a protein targeting to vacuole and part_of autophagy, i.e., the new term would get the parents that CVT pathway has now, and CVT pathway would just move down a notch. I think Val has some things that are involved in protein targeting in autophagy but aren't considered part of the CVT pathway, hence the slightly more general term.

cheers, m

Original comment by: mah11

[gocentral]

That is correct Val

Original comment by: ValWood

[gocentral]

I have another question/problem

I am finding it confusing that autophagosome= autophagic vacuole (exact synonym) and is a is_a child of vacuole

I thought an autophagasome and a vacuole were distict structures? (although autophagic bodies can accumulate in vacuoles)

and how can something be targeted to a structure, if it is already one?

also autophagic vacuole formation is not part of vacuole biogenesis, which if this arrangement was correct it presumably would be?

In summary I think we need a term whose primary name is "autphagosome" I'm not sure if autophagic vacuole is required, or not...or where

Original comment by: ValWood

[gocentral]

Sorry! I forgot to monitor this item after I commented initially. My only concern with the parentage is that there are also CVT gene products that are not involved in autophagy. Does the "CVT pathway" parentage to "protein targeting to vacuole involved in autophagy" create problems? This parentage issue may have existed before, but I will bring it up now anyway.

Also, re: autophagosome, it's my understanding that GO:5773 is a grouping term and since an autophagic vacuole is a kind of vacuole (by the GO definitions) isn't the current placement alright? The yeast vacuole that the autophagosome is being targeted to isn't GO:5773 but GO:324 "fungal-type vacuole". I'm also pretty sure that the autophagosome is referred to as the "autophagic vacuole" in other organisms and and so we do need the term (which one should be the term name and which the synonym I guess could be up for debate. I for one don't have an opinion on this.)

As for the parentage up to "vacuole biogenesis", I guess autophagic vacuole formation could be under there somewhere.

-Julie

Original comment by: juliep

[gocentral]

If there is a problem with the parentage of 'CVT pathway', it was there before the latest bit of work -- it was directly part_of autophagy before we added 'protein targeting to vacuole involved in autophagy'. We can move CVT pathway to be directly is_a protein targeting to vacuole, and not have any paths to autophagy, if that fits the biology better.

It is correct that an autophagic vacuole (by any name) is a subtype of vacuole; beyond that I don't think I can really help with the 'autophagic vacuole'/'autophagosome' question. We do seem to be a little inconsistent in whether we call it a type of vacuole (in CC, but with "vesicle" in the def ?!?) or a vesicle, but I can just fix that and make it a type of vacuole throughout.

m

Original comment by: mah11

[gocentral]

Yes ignore my vacuole comments. i forgot we now refer to vaculoe for yeast as fungal-type vacuole so I was thinking of "fungal-type vacuole" so the current "vacuole" parant isn't a problem.

Original comment by: ValWood

[gocentral]

OK. I've fixed the other things with CVT pathway and autophagic vac terms in BP and CC.

can we close? m

Original comment by: mah11

[gocentral]

Sigh, bummer that the CVT tpv got missed earlier. Thanks for fixing it now though.

It's okay by me to close. Rama?

-Julie

Original comment by: juliep

[gocentral]

Hi Midori, Julie,

Thanks for sorting through these. I was also concerned about the CVT pathway TPV. All good now. Can be closed.

Rama

Original comment by: rbalakri

[gocentral]

Great! Thanks everyone!

(Val - I know you'll open new items if anything else comes up ;) )

Original comment by: mah11

[gocentral]

• status: open --> closed-fixed

Original comment by: mah11

[gocentral]

• milestone: 224410 --> PomBase

Original comment by: mah11